Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018676.1 Corchorus olitorius cultivar O-4 contig18709, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 127677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:878 original size:17 final size:17
Alignment explanation
Indices: 856--894 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
846 ACTGCCTGCC
*
856 TTTTCTCCTCTTTCCTT
1 TTTTCTCCTCTTTCCAT
**
873 TTTTCTTTTCTTTCCAT
1 TTTTCTCCTCTTTCCAT
890 TTTTC
1 TTTTC
895 ACATTTTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTCTCCTCTTTCCAT
Found at i:925 original size:18 final size:18
Alignment explanation
Indices: 889--930 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
879 TTTCTTTCCA
*
889 TTTTTCACATTTTTCTTT
1 TTTTTCACATTTTTATTT
907 TTTTTCA-ATTTTTAATTT
1 TTTTTCACATTTTT-ATTT
925 TGTTTT
1 T-TTTT
931 TCACTAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 11 0.52
19 4 0.19
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTTCACATTTTTATTT
Found at i:11379 original size:29 final size:29
Alignment explanation
Indices: 11347--11408 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
11337 AAGACGAATA
***
11347 TATAGTATGGACAAAATTTAACCCGAAAC
1 TATAGTATGGACAAAAAAAAACCCGAAAC
* * *
11376 TATATTTTGGCCAAAAAAAAACCCGAAAC
1 TATAGTATGGACAAAAAAAAACCCGAAAC
11405 TATA
1 TATA
11409 TCACCCAAGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (29 bp):
TATAGTATGGACAAAAAAAAACCCGAAAC
Found at i:11538 original size:2 final size:2
Alignment explanation
Indices: 11531--11558 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11521 AATGACATGA
11531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11559 TATTTGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17765 original size:18 final size:19
Alignment explanation
Indices: 17742--17778 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
17732 CCATATATAT
17742 TATATAAGAT-ATAAGATA
1 TATATAAGATAATAAGATA
17760 TATATAAGATAATAAGATA
1 TATATAAGATAATAAGATA
17779 ATTTGATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (19 bp):
TATATAAGATAATAAGATA
Found at i:19310 original size:310 final size:309
Alignment explanation
Indices: 18749--19370 Score: 1127
Period size: 310 Copynumber: 2.0 Consensus size: 309
18739 TATAATATAT
*
18749 ACTAAATAGTATTTGAAAGACCTAGAGAATTTACCAAAGGCCCCTTTTGAGGATCGATGAGGAGG
1 ACTAAATAGTATTTGAAAGACCTAGAGAATTTACCAAAGGCCCCTTTTCAGGATCGATGAGGAGG
* *
18814 CTCCACTTTAACTTTTTTTGTCCTTTTCTGTCTTTTCTCACTTGCCAATTTACTAAGAAGACCAT
66 CTCCACTTGAACTTTTTTTGTCATTTTCTGTCTTTTCTCACTTGCCAATTTACTAAGAAGACCAT
* *
18879 AGGTTAGTTTCTAGCCAGTTCTTGCCTTTGAGCCATTTTTTGTAATTATCCTTTCCCTTTCACAT
131 AAGTTAGTTTCTAGCCAGTTCTTGCCCTTGAGCCATTTTTTGTAATTATCCTTTCCCTTTCACAT
18944 AAATGTTACAATAAATCCTATCCCTCTTAATTATCTAGAATTGTAACATCTCTTTAGGCCTTTCA
196 AAATGTTACAATAAATCCTATCCCTCTTAATTATCTAGAATTGTAACATCTCTTTAGGCCTTTCA
*
19009 TGTCTATATGAAGAAGAAAGTAAACTTAGTTTTTGTTTAAGTGCTACAC
261 TGTCTATATGAAGAAAAAAGTAAACTTAGTTTTTGTTTAAGTGCTACAC
* *
19058 ACTAAATAGTATTTGAAAGACCTAGGGAATTTACCAAAGTCCCCTTTTCAGGATCGATGAGGAGG
1 ACTAAATAGTATTTGAAAGACCTAGAGAATTTACCAAAGGCCCCTTTTCAGGATCGATGAGGAGG
* * *
19123 CTCCACTTGAACTTTTTTTTGTCATTTTTTGTCTTTTTTCACTTGCCAATTTACTAAGAAGACCC
66 CTCCACTTGAAC-TTTTTTTGTCATTTTCTGTCTTTTCTCACTTGCCAATTTACTAAGAAGACCA
*
19188 TAAGTTAGTTTCTAGCCAGTTCTTGCCCTTGAGCCCTTTTTTGTAATTATCCTTTCCCTTTCACA
130 TAAGTTAGTTTCTAGCCAGTTCTTGCCCTTGAGCCATTTTTTGTAATTATCCTTTCCCTTTCACA
19253 TAAATGTTACAATAAATCCTATCCCTCTTAATTATCTAGAATTGTAACATCTCTTTAGGCCTTTC
195 TAAATGTTACAATAAATCCTATCCCTCTTAATTATCTAGAATTGTAACATCTCTTTAGGCCTTTC
19318 ATGTCTATATGAAGAAAAAAGTAAACTTAGTTTTTGTTTAAGTGCTACAC
260 ATGTCTATATGAAGAAAAAAGTAAACTTAGTTTTTGTTTAAGTGCTACAC
19368 ACT
1 ACT
19371 TTAGAGGAGG
Statistics
Matches: 300, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
309 73 0.24
310 227 0.76
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (309 bp):
ACTAAATAGTATTTGAAAGACCTAGAGAATTTACCAAAGGCCCCTTTTCAGGATCGATGAGGAGG
CTCCACTTGAACTTTTTTTGTCATTTTCTGTCTTTTCTCACTTGCCAATTTACTAAGAAGACCAT
AAGTTAGTTTCTAGCCAGTTCTTGCCCTTGAGCCATTTTTTGTAATTATCCTTTCCCTTTCACAT
AAATGTTACAATAAATCCTATCCCTCTTAATTATCTAGAATTGTAACATCTCTTTAGGCCTTTCA
TGTCTATATGAAGAAAAAAGTAAACTTAGTTTTTGTTTAAGTGCTACAC
Found at i:27114 original size:5 final size:6
Alignment explanation
Indices: 27098--27122 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27088 CCTTTATTAT
27098 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
27123 TTGGGGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:27373 original size:3 final size:3
Alignment explanation
Indices: 27365--27394 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
27355 TTCTTTCGAT
27365 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
27395 CCTCCCTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:29875 original size:29 final size:30
Alignment explanation
Indices: 29815--29889 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
29805 TTAATGTTTG
**
29815 ATTTCCTGTGGGAATTTTTTTTTTTGGCCAA
1 ATTTCCTGTGGGAA-TAATTTTTTTGGCCAA
29846 ATTTCCTGTGGGAA-AATTTTTTTGGCCAA
1 ATTTCCTGTGGGAATAATTTTTTTGGCCAA
*
29875 ATTCCCTGTGGGAAT
1 ATTTCCTGTGGGAAT
29890 GATGGAGGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 26 0.65
31 14 0.35
ACGTcount: A:0.20, C:0.15, G:0.21, T:0.44
Consensus pattern (30 bp):
ATTTCCTGTGGGAATAATTTTTTTGGCCAA
Found at i:32825 original size:6 final size:6
Alignment explanation
Indices: 32814--32853 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
32804 TTTTGGACTG
32814 CTCTGC CTCTGC CTCTGC CTCTGC CTCTGC CTCTGC CTCT
1 CTCTGC CTCTGC CTCTGC CTCTGC CTCTGC CTCTGC CTCT
32854 AAAGTTGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.15, T:0.35
Consensus pattern (6 bp):
CTCTGC
Found at i:39718 original size:124 final size:127
Alignment explanation
Indices: 39571--39826 Score: 421
Period size: 124 Copynumber: 2.0 Consensus size: 127
39561 CATTGTTTAA
*
39571 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-C-AT-TA-
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTATCTAT
39632 TAATTTTTACCATTTTACTATTTTAATTGAAAAAACTTATATATATTAGAATTTTTTAAATAT
66 TAATTTTTACCATTTTACTATTTTAATT-AAAAAACTTATATATATTAGAATTTTTTAAATAT
39695 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCC-TAT--C
*
39760 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
63 TA-TTAATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATA
39825 T
127 T
39826 A
1 A
39827 TTTCTTAAAT
Statistics
Matches: 122, Mismatches: 2, Indels: 9
0.92 0.02 0.07
Matches are distributed among these distances:
124 55 0.45
125 1 0.01
127 2 0.02
130 2 0.02
131 35 0.29
132 27 0.22
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (127 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTATCTAT
TAATTTTTACCATTTTACTATTTTAATTAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:49592 original size:18 final size:18
Alignment explanation
Indices: 49565--49605 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
49555 CTAGCTCATG
49565 TTCA-TATCATCT-CCATT
1 TTCACTATCAT-TGCCATT
49582 TTCACTATCATTGCCATT
1 TTCACTATCATTGCCATT
*
49600 CTCACT
1 TTCACT
49606 CTCAGTGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.22, C:0.32, G:0.02, T:0.44
Consensus pattern (18 bp):
TTCACTATCATTGCCATT
Found at i:49718 original size:21 final size:21
Alignment explanation
Indices: 49694--49735 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
49684 GATAGAAGCC
49694 AACATAACAGGGAGAATATTT
1 AACATAACAGGGAGAATATTT
*
49715 AACATACCAGGGAGAATATTT
1 AACATAACAGGGAGAATATTT
49736 GACAATGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (21 bp):
AACATAACAGGGAGAATATTT
Found at i:50021 original size:22 final size:22
Alignment explanation
Indices: 49995--50043 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
49985 TTCAAATAAA
49995 ATGTAATAAATATGCTGCAATC
1 ATGTAATAAATATGCTGCAATC
*
50017 ATGTAATAAATGTGCTGCAATC
1 ATGTAATAAATATGCTGCAATC
50039 ATGTA
1 ATGTA
50044 TTTAAAGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (22 bp):
ATGTAATAAATATGCTGCAATC
Found at i:55103 original size:42 final size:42
Alignment explanation
Indices: 55047--55127 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
55037 GTGTTTAGCT
*
55047 TAATGTGTCTCGTGTCCGAATCGTGTC-AGACACGATTATGG
1 TAATGTGTCTCGTGTCAGAATCGTGTCAAGACACGATTATGG
* *
55088 TAATCGTGTTTCGTGTCATAATCGTGTCAAGACACGATTA
1 TAAT-GTGTCTCGTGTCAGAATCGTGTCAAGACACGATTA
55128 ACACGTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
41 4 0.11
42 20 0.57
43 11 0.31
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (42 bp):
TAATGTGTCTCGTGTCAGAATCGTGTCAAGACACGATTATGG
Found at i:55534 original size:12 final size:12
Alignment explanation
Indices: 55517--55548 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
55507 TACCCTATGT
55517 AAACACGACACG
1 AAACACGACACG
55529 AAACACGACACG
1 AAACACGACACG
55541 AAACACGA
1 AAACACGA
55549 ATTGCCAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.31, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:61592 original size:6 final size:6
Alignment explanation
Indices: 61581--61614 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
61571 ATTTAGTCTT
61581 ATAAAG ATAAAG ATAAA- ATAAAG ATAAAG ATAAA
1 ATAAAG ATAAAG ATAAAG ATAAAG ATAAAG ATAAA
61615 TGAATCCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (6 bp):
ATAAAG
Found at i:61603 original size:17 final size:17
Alignment explanation
Indices: 61581--61614 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
61571 ATTTAGTCTT
61581 ATAAAGATAAAGATAAA
1 ATAAAGATAAAGATAAA
61598 ATAAAGATAAAGATAAA
1 ATAAAGATAAAGATAAA
61615 TGAATCCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.18
Consensus pattern (17 bp):
ATAAAGATAAAGATAAA
Found at i:70293 original size:11 final size:10
Alignment explanation
Indices: 70268--70292 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
70258 AGCGTAAAAG
70268 CCCCCTCCCC
1 CCCCCTCCCC
70278 CCCCCTCCCC
1 CCCCCTCCCC
70288 CCCCC
1 CCCCC
70293 CCCAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.92, G:0.00, T:0.08
Consensus pattern (10 bp):
CCCCCTCCCC
Found at i:71474 original size:21 final size:21
Alignment explanation
Indices: 71417--71475 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 21
71407 TTTTAGAGAA
*
71417 TAAATCATTTTAACATATAAC
1 TAAATCATTTTAGCATATAAC
*
71438 TAAATATTTCAATTTAGCATATAAC
1 T-AA-A--TCATTTTAGCATATAAC
71463 TAAATCATTTTAG
1 TAAATCATTTTAG
71476 AGAATACACC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
21 9 0.29
22 2 0.06
23 2 0.06
24 2 0.06
25 16 0.52
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (21 bp):
TAAATCATTTTAGCATATAAC
Found at i:71864 original size:213 final size:213
Alignment explanation
Indices: 71478--71871 Score: 628
Period size: 213 Copynumber: 1.8 Consensus size: 213
71468 CATTTTAGAG
*
71478 AATACACCATCAGTGGAGTTTAGCAGACTACACATGCGGGTCTGAAGGGTGAGGACATGTGTCCT
1 AATACACCATCAGTGGAGTTTAGCAGACTACACAAGCGGGTCTGAAGGGT--GGACATGTGTCCT
*
71543 CTAGGAACTAAATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATGTGTCAACTCCAC
64 CTAGGAACTAAATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATATGTCAACTCCAC
* *
71608 AACCCACTTGTGGAGTCCAAAATTTACACCGCCGGTATATCAAATAATTACCTTATGTTTAAATA
129 AACCCACTTGTGGAGTCCAAAATTTACACCACCGATATATCAAATAATTACCTTATGTTTAAATA
71673 TTGTTTATGGGTTTATATAT
194 TTGTTTATGGGTTTATATAT
* * * *
71693 AATACATCGTCAGTGGAGTTTAGCAGACTGCACAAGCGGGTCTTGAAGGGT-GACATGTGTCCTT
1 AATACACCATCAGTGGAGTTTAGCAGACTACACAAGCGGGTC-TGAAGGGTGGACATGTGTCCTC
* * * * *
71757 TAGGGACTAGATTGAAATATTTAAAATTTAATTAATTCAGAAAATGGACATATGTCAACTCCATA
65 TAGGAACTAAATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATATGTCAACTCCACA
*
71822 ACCCACTTGTGGAGTCCAAAATTTACACCACCGATGTATCAAATAATTAC
130 ACCCACTTGTGGAGTCCAAAATTTACACCACCGATATATCAAATAATTAC
71872 TCATTATTTA
Statistics
Matches: 164, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
213 118 0.72
215 38 0.23
216 8 0.05
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (213 bp):
AATACACCATCAGTGGAGTTTAGCAGACTACACAAGCGGGTCTGAAGGGTGGACATGTGTCCTCT
AGGAACTAAATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATATGTCAACTCCACAA
CCCACTTGTGGAGTCCAAAATTTACACCACCGATATATCAAATAATTACCTTATGTTTAAATATT
GTTTATGGGTTTATATAT
Found at i:75326 original size:2 final size:2
Alignment explanation
Indices: 75319--75350 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
75309 AAACAGAGGA
75319 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
75351 CCTTCTTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85170 original size:5 final size:5
Alignment explanation
Indices: 85162--85197 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
85152 TTTTTTTATT
85162 TTTTA TTTTA TTTTA TTTTA -TTTA -TTTA -TTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
85198 TTGCTGGTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 12 0.40
5 18 0.60
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:85175 original size:10 final size:9
Alignment explanation
Indices: 85152--85197 Score: 55
Period size: 8 Copynumber: 5.4 Consensus size: 9
85142 CTTCTTCTTC
85152 TTTT-TTTA
1 TTTTATTTA
85160 -TTT-TTTA
1 TTTTATTTA
85167 TTTTATTTTA
1 TTTTA-TTTA
85177 TTTTATTTA
1 TTTTATTTA
85186 -TTTATTTA
1 TTTTATTTA
85194 TTTT
1 TTTT
85198 TTGCTGGTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.21
8 11 0.32
9 7 0.21
10 9 0.26
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTATTTA
Found at i:85180 original size:22 final size:22
Alignment explanation
Indices: 85155--85197 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
85145 CTTCTTCTTT
85155 TTTTATTT-TTTATTTTATTTTA
1 TTTTATTTATTTA-TTTATTTTA
85177 TTTTATTTATTTATTTATTTT
1 TTTTATTTATTTATTTATTTT
85198 TTGCTGGTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTATTTATTTATTTATTTTA
Found at i:89516 original size:106 final size:108
Alignment explanation
Indices: 89324--89530 Score: 321
Period size: 106 Copynumber: 1.9 Consensus size: 108
89314 CCAGGAAAAC
* *
89324 ACCATTTCTGGCCATCCTCTCTTCCTTTTGTCCCTTAATTCGTCTTCTTTCTCCCTTTTCTTATT
1 ACCATTTCCGGCCATCCTCTCTTCCTTTTGT-CCTTAATTCGTCTTCTTTCTCCCTTTTCTTACT
*
89389 TTTCTTATCAAAAATAGAGTTTTCCCAATATTCAAAGCGACAAT
65 TTTCTTATCAAAAATAAAGTTTTCCCAATATTCAAAGCGACAAT
* *
89433 ACCATTTCCGGCCATCCTCTCTAT-CTTTTGT-C-TAATTTGTCTTCTTTCTCCCTTTTCTTGCT
1 ACCATTTCCGGCCATCCTCTCT-TCCTTTTGTCCTTAATTCGTCTTCTTTCTCCCTTTTCTTACT
*
89495 TTTCTTATCAAATATAAAGTTTTCCCAATATTCAAA
65 TTTCTTATCAAAAATAAAGTTTTCCCAATATTCAAA
89531 ACCCAAAAAG
Statistics
Matches: 91, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
106 61 0.67
107 1 0.01
109 28 0.31
110 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.07, T:0.45
Consensus pattern (108 bp):
ACCATTTCCGGCCATCCTCTCTTCCTTTTGTCCTTAATTCGTCTTCTTTCTCCCTTTTCTTACTT
TTCTTATCAAAAATAAAGTTTTCCCAATATTCAAAGCGACAAT
Found at i:95818 original size:27 final size:27
Alignment explanation
Indices: 95776--95829 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
95766 GTCGGTTTAG
95776 GAGGGAAATAGCCGTTGTAATTTCTGC
1 GAGGGAAATAGCCGTTGTAATTTCTGC
*
95803 GAGGGAAATAGTCGTTGTAATTTCTGC
1 GAGGGAAATAGCCGTTGTAATTTCTGC
95830 TGTTTAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.31
Consensus pattern (27 bp):
GAGGGAAATAGCCGTTGTAATTTCTGC
Found at i:96066 original size:2 final size:2
Alignment explanation
Indices: 96059--96101 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
96049 ATTCCCAAGG
96059 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
96101 T
1 T
96102 GTATTCTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:102345 original size:29 final size:30
Alignment explanation
Indices: 102312--102369 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
102302 TATAAATAAT
* *
102312 ATAATATAATT-AGATAA-TTATATTTATAC
1 ATAATAAAATTGA-ATAATTTATATGTATAC
102341 ATAATAAAATTGAATAATTTATATGTATA
1 ATAATAAAATTGAATAATTTATATGTATA
102370 TATTAATTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (30 bp):
ATAATAAAATTGAATAATTTATATGTATAC
Found at i:102495 original size:26 final size:26
Alignment explanation
Indices: 102470--102518 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
102460 TTAATGTTTA
102470 AATT-TTATTTT-TTATTAAAAAATTT
1 AATTATTATTTTATT-TTAAAAAATTT
102495 AATTATTATTTTATTTTAAAAAAT
1 AATTATTATTTTATTTTAAAAAAT
102519 AAATATGGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.18
26 16 0.73
27 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AATTATTATTTTATTTTAAAAAATTT
Found at i:122262 original size:11 final size:11
Alignment explanation
Indices: 122225--122262 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
122215 CGATTATATA
*
122225 AAATAAATTAT
1 AAATTAATTAT
122236 CAAA-TAATTAT
1 -AAATTAATTAT
122247 AAATTAATTAT
1 AAATTAATTAT
122258 AAATT
1 AAATT
122263 TCATTTCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:122671 original size:82 final size:83
Alignment explanation
Indices: 122518--122684 Score: 214
Period size: 82 Copynumber: 2.0 Consensus size: 83
122508 CAATAGTAAA
* * * *
122518 TCTCGGATTTCAAGATGCGTCAGGCAATTACTGAATATAGTAAATTTCGGATTACAGGACATGTC
1 TCTCGAATTTCAAGACGCGTCAGGCAACTAC-GAATATAGTAAATCTCGGATTACAGGACATGTC
122583 AGACAGATATAGTATAATG
65 AGACAGATATAGTATAATG
* * *
122602 TCTCGAATTTCAAGACGCGTCAGGCAGCTAC-AGTATAGTAAATCTCGGATTTCAAGG-CACT-T
1 TCTCGAATTTCAAGACGCGTCAGGCAACTACGAATATAGTAAATCTCGGATTAC-AGGACA-TGT
*
122664 TAGACAGATATAGTATAATG
64 CAGACAGATATAGTATAATG
122684 T
1 T
122685 AACCTGAAGT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
82 42 0.58
83 4 0.05
84 27 0.37
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (83 bp):
TCTCGAATTTCAAGACGCGTCAGGCAACTACGAATATAGTAAATCTCGGATTACAGGACATGTCA
GACAGATATAGTATAATG
Done.